NCSI: Molecular Dynamics Simulations of Gap Junction Intercellular Channels

Status	Completed
Mentor Name	Steve Reichow
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	1-2 years
Project Title	Molecular Dynamics Simulations of Gap Junction Intercellular Channels
Summary	The Reichow lab uses cryo-electron microscopy (CryoEM) and molecular dynamics (MD) simulations to understand the fundamental relationship between structure, dynamics and function in complex biomolecular systems. Gap junctions are large pore-forming membrane channels that span the membranes of two neighboring cells, connecting their cytosols to facilitate cell-to-cell communication. We aim to use GPU-accelerated MD simulations to understand the molecular requirements underlying solute permeation through these intercellular channels.
Job Description	The student will use the scripting language TK/Tcl, along with the program visual molecular dynamics (VMD) to prepare gap junction simulation systems. They will then perform all-atom equilibrium MD simulations using the nanoscale molecular dynamics (NAMD) engine to simulate gap junctions in multiple conductance states. The student will then be expected to write analytical scripts in Tcl, Python, and BASH to extract data from the simulations, and analyze the data using standard scientific libraries such as numpy, pandas, and matplotlib in addition to biophysical libraries, such as MDAnalysis and Modeller.
Computational Resources	Our laboratory has access to the GPU-nodes on SDSU-Comet and PSC-Bridges. Each node on Comet contains dual Xeon CPUs, with four Nvidia-P100 GPUs. Each node on PSC-Bridges contains dual Xeon CPUs, with two Nvidia-P100 GPUs. We have allocated storage on SDSU-Oasis and PSC-Pylon. The student will also have access to PSU’s COEUS cluster, OHSU’s Exacloud cluster, and local workstations for simulation and data analysis. This work will build off of simulations done under our start-up XSEDE allocation (Dynamic Mechanisms of Membrane Channel Gating). An XSEDE resource allocation is under preparation and will be submitted for the Winter deadline (Sep-15).
Contribution to Community
Position Type	Intern
Training Plan	The training plan will include regular (daily) meetings with a lead graduate student to discuss research agenda and data analysis. In addition, the trainee will meet with the PI on a weekly basis to discuss on-going research and professional development plans. Furthermore, the trainee will gain experience in the dissemination of research through participation in weekly group meetings, and local and regional symposiums/conferences, and contribute to the preparation (authorship) of manuscripts for publication. Technical Training: The student will be trained on the application of advanced molecular dynamics techniques/theories such as: constant electric field simulations, Markov-State Models, and free-energy calculations, and gain experience using scripting languages to conduct advanced data analysis routines. The student will also be trained to manipulate molecules and render professional images with VMD.
Student Prerequisites/Conditions/Qualifications	The student is expected to conduct independent research with demonstrated experience with Python, TK/Tcl and Bash scripting languages, and MD simulation software (e.g., NAMD, GROMACS, VMD, etc.).
Duration	Quarter
Start Date	09/28/2020
End Date	12/06/2020